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Software

SiPSiC: https://bioconductor.org/packages/release/bioc/html/SiPSiC.html

Pathifier: https://www.bioconductor.org/packages/release/bioc/html/pathifier.html

Datasets

H3K27ac ChIP-seq and RNA-seq of lung neuroendocrine tumors:

UCSC genome browser: https://genome-euro.ucsc.edu/s/yotamd/lung_NET

GEO (processed data): https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE247574

EGA (raw data): https://ega-archive.org/datasets/EGAD50000000083

RNA-seq and H3K27ac and H3K4me2 ChIP-seq of ileal and pancreatic neuroendocrine tumors:

GEO (processed data): https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE116356

dbGaP (raw data): https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001910.v1.p1

Single cell RNA-seq data:

HPV-related multiphenotypic sinonasal carcinoma: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?&acc=GSE293187

Adenoid cystic carcinoma: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE210171

Early T-cell progenitor acute lymphoblastic leukemia: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE161901

Gastrointestinal stromal tumors:

GEO (processed data): https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE107447

dbGaP (raw data): https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001906.v1.p1

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